


Dr. Jackson Goes to Atlantis

by whimsicalwhims



Category: Stargate Atlantis, Stargate SG-1
Genre: M/M
Language: English
Status: Completed
Published: 2008-12-13
Updated: 2008-12-13
Packaged: 2017-12-08 05:56:39
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 1,534
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/757860
Author URL: https://archiveofourown.org/users/whimsicalwhims/pseuds/whimsicalwhims
Summary: <blockquote class="userstuff">
              <p>Dr. Daniel Jackson is put in charge of Atlantis.</p>
            </blockquote>





	Dr. Jackson Goes to Atlantis

**Author's Note:**

> **Timeline:** Vague mentions of SGA season 5 events, but nothing very specific.  
>  **Archive Rights:** No. Please do not take this story and post it elsewhere.  
>  **Disclaimer:** I do not own SG-1, SGA, or any of the characters and situations depicted on the shows. No profit is being made from this and no infringement is intended.  
>  **A/N:** Written for iamrosalita for the lilblckdressfic ficathon. The prompts I used were "post-breakup with Jack" and "Daniel in charge of Atlantis."

John had always figured Daniel Jackson would come back to Atlantis again--it’s practically the guy’s Mecca after all--but John had never quite imagined this. In John’s head, Dr. Daniel Jackson always returned as a resident archaeologist, or as the head of a newly-established department whose main focus was to study the Ancients. Jackson would spend his days pouring over texts, pursing his lips as he came across a new puzzle; tugging at his bed-mused hair as he--

Right. John shakes off the thought. John’s brother once accused him of having an overactive imagination. Not that John will ever admit it to anyone, but he half suspects his brother was right. The point being, however, that even when John laid awake at night, never once did he imagine that Jackson would return to Atlantis as their new leader.

“He’s no Woolsey, that’s for sure,” John says to Rodney as they stand in the tower, watching Jackson being greeted by the personnel in the gate room. John had offered his congratulations on the new job when Jackson first arrived, staying only a few minutes before making up some excuse about pressing paperwork. 

“I liked Woolsey,” Rodney says between a mouthful of tortilla chips. 

John shoots Rodney an incredulous look. “No, you didn’t.”

“Well, he had his moments. I don’t see why the IOA decided to go ahead and replace him anyway. Sure, Daniel might know a thing or two about the Ancients--”

John holds back a snort.

“But that doesn’t mean he should be in charge of Atlantis.”

John shakes his head. Once Rodney gets going, there’s no stopping him. He snatches the bag of chips, ignoring Rodney’s protests as he pretends to read the ingredients. “You know,” he says, “ I think these have lime in them.”

John tries to hide his grin as Rodney heads off towards the infirmary. Though Rodney’s parting glare tells him that he’s probably not that successful. 

Oh, well, John thinks as he turns his attention back down to where Jackson is shaking Lorne’s hand. John appreciates Jackson’s desire to get to know his new people. Though the spark that John feels when Jackson’s gaze meets his--well, that’s something that John could live without.

***

Jackson asks John to teach him Athosian stick fighting. 

“Why not Teyla?” John asks. “She’s the expert.” And not that John will ever actually say it--because everyone already knows it anyway--but she’s ten times better at it than John will ever be.

Jackson practically smiles at that: a quick upturn to his lips that tells John that Jackson knows what he’s thinking. “I already tried that,” he says. “Yesterday.” Jackson rubs at his hip, an offhand gesture that John suspects Jackson doesn’t even know he’s making. Still, John has to fight with himself not to stare. Jackson continues, “I’m afraid I’m not ready for the advanced course just yet.”

John pictures it in his mind: The two of them, hot and sweaty, trying to hit each other with sticks. Maybe with some grunting and gasping thrown in. John can’t decide if it’s his worst nightmare or a dream come true.

“Okay,” John agrees before he can give himself a chance to change his mind.

This time, the smile on Jackson’s face is unmistakable. 

***

It’s been three weeks and four days since Daniel Jackson came to Atlantis, and so far, there have been no major intergalactic incidences. (Unless you count the hours John’s spent going over paperwork with Jackson in his office. Which John doesn’t, because it’s all part of his job, and the fact that he never spent this much time with Woolsey doesn’t count either.) Of course, nothing good lasts forever. 

John’s team has just returned from an off-world mission when Atlantis gets the news. Lorne’s team has been taken by the Wraith, and unless Atlantis will hand over Dr. Keller and all of the research on the enzyme, Lorne and his team will be dead within twenty-four hours.

They quickly plan a rescue mission, a plan that does not involve trading hostages, think you very much. 

“I’m going with you,” Jackson says as they dial the gate.

John slowly counts to ten. And does it again. “You’re the leader of Atlantis. You don’t get to be the one risking your life.”

Jackson looks pissed off, but John really doesn’t care right now. 

“I have plenty of negotiation experience,” Jackson says. “And a lot more combat experience than McKay.”

Ignoring Rodney’s protests, John shakes his head. Elizabeth was an expert negotiator too, and look where that got her. John knows, from reading the files, that Jackson has a “jump first, look later” philosophy. While John appreciates that in the abstract sense, he’s not going to have Jackson along on missions unless absolutely necessary. And while Jackson may be the one officially in charge, John’s still the military commander.

“We need you here,” John says. “In case something goes wrong.”

John turns to leave, breathing a sigh of relief when Jackson doesn’t push the issue even farther. He doesn’t know how General O’Neill managed it for close to ten years.

 

***

In the end, it takes two days, another hostage situation, a few minor wounds, and Jackson having to contact the Wraith before the situation is resolved.

“Come see me when you get out of the infirmary,” Jackson tells John as Keller finishes stitching up John’s arm.

Keller releases John as soon as the last stitch is tied, with specific orders not to get the stitches wet for a few days, and John heads towards Jackson’s quarters.

John only has to knock once before Jackson opens the door. John hasn’t been in the room since they boxed up Elizabeth’s possessions, and he’s surprised to find that being here again doesn’t hurt as much as he thought it would. The walls are bare--no Johnny Cash posters here--but the tables and bed are covered with books and scrolls. 

Jackson pushes a pile of books aside and gestures for John to have a seat on the bed. Jackson sits down next to him and John has to remind himself not to fidget as Jackson studies him. Because, massive crush aside, John’s not sure he wants to be the focus of Jackson’s quiet intensity. 

“Is what happened earlier going to be a pattern?” Jackson’s question breaks the silence.

“Probably,” John admits, too tired to dance around the issue. “You dictate policy and report back to the IOA, but I make the decisions on the military issues.”

“So what you’re saying is that I’m an impotent leader.”

John really hopes not. “I wouldn’t say that.” He smiles, and damn it, he knows he’s flirting.

Jackson laughs. “A poor choice of words. I didn’t ask for this job, you know. I was surprised when the IOA offered it to me.”

John had been wondering about that. The IOA wanted Atlantis under its thumb, and nothing in Jackson’s career even hinted that he would be compliant.

“Jack pulled some strings. I think--” He pauses, swallowing. “I think it was Jack’s way of doing penance.”

“For breaking your heart.” It’s only a guess, but it makes the most sense.

Jackson thinks for a moment, removing his glasses as he answers, “Jack likes to think that nobody knows. Knew.”

John could say so many things right now: “You only had to watch the two of you together to know” or “O’Neill’s an idiot.” But his heart’s racing and Jackson’s eyes are slightly dilated, so he swallows back the words and does something even better.

Jackson’s lips are soft against his. John holds his breath, almost afraid to move because he’s concerned he read this wrong. But then Jackson kisses him back, deepening the kiss as he pushes John back onto the bed.

“I don’t want to be a rebound fuck,” John manages as Jackson runs his hand up John’s thigh. 

“This isn’t.” Jackson leans in and kisses John’s mouth again. “You’re not.”

 

***

When Rodney starts complaining that John hasn’t shown up to their midnight car races in a while, John figures that he should at least put in an appearance. But it’s not as though John doesn’t know that Rodney has also been preoccupied as of late. 

“You’ve been spending a lot of time with Daniel lately,” Rodney says as he tries to make his car run John’s into the wall.

“There’s been a lot to do.” John evades Rodney’s maneuver, pulling his car into the lead.

Something in John’s voice must have given him away. Rodney’s look is accusatory as he ignores the race for a moment. Rodney points a finger at him. “You’ve been Jacksonized!”

“Is that even a word?”

“I’ve seen it before. A thousand times.”

John doubts that.

“Before long, he gets everyone worshipping at his feet, practically in love with him.”

John studies the controller in his hand, trying to search for an answer. 

“Oh my God.” Rodney almost drops his own controller. “You’re in love with him. Everything is starting to make sense now.” 

John simply shrugs. “I can still beat you at this.” He starts his car down the hallway again.

“Somebody’s clearly delusional,” Rodney says, turning his attention back to the game.


End file.
